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Haga IR, Shih BB, Tore G, Polo N, Ribeca P, Gombo-Ochir D, Shura G, Tserenchimed T, Enkhbold B, Purevtseren D, Ulziibat G, Damdinjav B, Yimer L, Bari FD, Gizaw D, Adedeji AJ, Atai RB, Adole JA, Dogonyaro BB, Kumarawadu PL, Batten C, Corla A, Freimanis GL, Tennakoon C, Law A, Lycett S, Downing T, Beard PM. Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa. Viruses 2024; 16:557. [PMID: 38675899 PMCID: PMC11053774 DOI: 10.3390/v16040557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the Poxviridae family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from the Pirbright Institute virus archive, and field isolates from recent disease outbreaks in Sri Lanka, Mongolia, Nigeria and Ethiopia. These genome sequences were compared to published genomes and classified into different subgroups. Two subgroups contained vaccine or vaccine-like samples ("Neethling-like" clade 1.1 and "Kenya-like" subgroup, clade 1.2.2). One subgroup was associated with outbreaks of LSD in the Middle East/Europe (clade 1.2.1) and a previously unreported subgroup originated from cases of LSD in west and central Africa (clade 1.2.3). Isolates were also identified that contained a mix of genes from both wildtype and vaccine samples (vaccine-like recombinants, grouped in clade 2). Whole genome sequencing and analysis of LSDV strains isolated from different regions of Africa, Europe and Asia have provided new knowledge of the drivers of LSDV emergence, and will inform future disease control strategies.
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Grants
- BB/R002606/1, BB/R008833/1, BB/X011038/1, BB/X011046/1, BB/CCG2250, BB/CCG1780/1, BBS/E/RL/230002C, BBS/E/RL/230002D, , BBS/E/I/00007039, /1, BB/IDG2250/1, Biotechnology and Biological Sciences Research Council
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Affiliation(s)
- Ismar R. Haga
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Barbara B. Shih
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK
| | - Gessica Tore
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Noemi Polo
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Paolo Ribeca
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
- UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, Mathematics Institute, Zeeman Builing, University of Warwick, Coventry CV4 7AL, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Ronald Ross Building, University of Liverpool, Liverpool L69 7BE, UK
- Biomathematics and Statistics Scotland, James Maxwell Clerk Building, Peter Guthrie Tait Road, Kings Buildings, Edinburgh EH9 3FD, UK
| | - Delgerzul Gombo-Ochir
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Gansukh Shura
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Tsagaan Tserenchimed
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Bazarragchaa Enkhbold
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Dulam Purevtseren
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Gerelmaa Ulziibat
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Batchuluun Damdinjav
- General Authority for Veterinary Service, Ministry of Food, Agriculture and Light Industry, Ulaanbaatar 13381, Mongolia;
| | - Lama Yimer
- School of Veterinary Medicine, Wollega University, Nekemte P.O. Box 395, Ethiopia;
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia;
| | - Fufa D. Bari
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia;
| | - Daniel Gizaw
- Animal Health Institute (AHI), Sebata P.O. Box 04, Ethiopia;
| | - Adeyinka Jeremy Adedeji
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | - Rebecca Bitiyong Atai
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | - Jolly Amoche Adole
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | | | | | - Carrie Batten
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Amanda Corla
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Graham L. Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Chandana Tennakoon
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Andy Law
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
| | - Tim Downing
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Philippa M. Beard
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
- School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK
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Enkhbold B, Shatar M, Wakamori S, Tamura T, Hiono T, Matsuno K, Okamatsu M, Umemura T, Damdinjav B, Sakoda Y. Genetic and virulence characterization of classical swine fever viruses isolated in Mongolia from 2007 to 2015. Virus Genes 2017; 53:418-425. [PMID: 28260187 DOI: 10.1007/s11262-017-1442-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/27/2017] [Indexed: 11/30/2022]
Abstract
Classical swine fever (CSF), a highly contagious viral disease affecting domestic and wild pigs in many developing countries, is now considered endemic in Mongolia, with 14 recent outbreaks in 2007, 2008, 2011, 2012, 2014, and 2015. For the first time, CSF viruses isolated from these 14 outbreaks were analyzed to assess their molecular epidemiology and pathogenicity in pigs. Based on the nucleotide sequences of their 5'-untranslated region, isolates were phylogenetically classified as either sub-genotypes 2.1b or 2.2, and the 2014 and 2015 isolates, which were classified as 2.1b, were closely related to isolates from China and Korea. In addition, at least three different viruses classified as 2.1b circulated in Mongolia. Experimental infection of the representative isolate in 2014 demonstrated moderate pathogenicity in 4-week-old pigs, with relatively mild clinical signs. Understanding the diversity of circulating CSF viruses gleans insight into disease dynamics and evolution, and may inform the design of effective CSF control strategies in Mongolia.
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Affiliation(s)
- Bazarragchaa Enkhbold
- Transboundary Animal Viral Diseases Diagnosis and Surveillance Unit, State Central Veterinary Laboratory, Ulaanbaatar, 17026, Mongolia
| | - Munkhduuren Shatar
- Transboundary Animal Viral Diseases Diagnosis and Surveillance Unit, State Central Veterinary Laboratory, Ulaanbaatar, 17026, Mongolia
| | - Shiho Wakamori
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan
| | - Tomokazu Tamura
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takahiro Hiono
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan
| | - Keita Matsuno
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0020, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan
| | - Takashi Umemura
- School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, 17026, Mongolia
| | - Batchuluun Damdinjav
- Transboundary Animal Viral Diseases Diagnosis and Surveillance Unit, State Central Veterinary Laboratory, Ulaanbaatar, 17026, Mongolia
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, 060-0818, Japan.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, 001-0020, Japan.
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